So my son's switch is now nearly identical to the new one we got. Which is to say both induce a LITTLE eyestrain. After some hours of playing Zelda: Breath of the Wild my eyes were definitely tired. Similar to the strain I used to get after spending 2-3 hours playing Destiny 2 on the XBox One. In other words, totally manageable. I suspect that there was a system update that made it a little worse, and that the new unit had already been updated (or had been updated first). I'll keep testing and let you guys know.
One thing for certain on the switch is that the "adaptive brightness" - which should only work when it's handheld - actually works when docked too. So it makes the display brighter and/or darker based on ambient light. I have NO idea how this even works when docked, since ostensibly the light sensors would be covered? What I can say is that there was a CLEAR difference in output (with the setting 'on' the display was brighter, sharper, and also hurt more) until we disabled that setting and then there was very little difference.